title: Survey of genes involved in rice secondary cell wall formation through a co-expression network.
abstract: The plant secondary cell wall is the major source of lignocellulosic biomass, a renewable energy resource that can be used for bioethanol production. To comprehensively identify transcription factors (TFs), glycosyltransferase (GT) and glycosyl hydrolase (GH) involved in secondary cell wall formation in rice (Oryza sativa), co-expression network analysis was performed using 68 microarray data points for different rice tissues and stages. In addition to rice genes encoding orthologs of Arabidopsis thaliana TFs known to regulate secondary cell wall formation, the network analysis suggested many novel TF genes likely to be involved in cell wall formation. In the accompanying paper (Hirano et al.), several of these TFs are shown to be involved in rice secondary cell wall formation. Based on a comparison of the rice and Arabidopsis networks, TFs were classified as common to both species or specific to each plant species, suggesting that in addition to a common transcriptional regulatory mechanism of cell wall formation, the two plants may also use species-specific groups of TFs during secondary wall formation. Similarly, genes encoding GT and GH were also classified as genes showing species-common or species-specific expression patterns. In addition, genes for primary or secondary cell wall formation were also suggested. The list of rice TF, GT and GH genes provides an opportunity to unveil the regulation of secondary cell wall formation in grasses, leading to optimization of the cell wall for biofuel production.
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, Japan.
authors.forename: Ko
authors.initials: K
authors.lastname: Hirano
authors.forename: Koichiro
authors.initials: K
authors.lastname: Aya
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Morinaka
authors.forename: Shiro
authors.initials: S
authors.lastname: Nagamatsu
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Sato
authors.forename: Baltazar A
authors.initials: BA
authors.lastname: Antonio
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Namiki
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Nagamura
authors.forename: Makoto
authors.initials: M
authors.lastname: Matsuoka
mesh_terms: D002473:Cell Wall / Q000378:metabolism*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D006026:Glycoside Hydrolases / Q000235:genetics / Q000378:metabolism; D016695:Glycosyltransferases / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D012275:Oryza / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018547:Plant Stems / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors; D016695:Glycosyltransferases; D006026:Glycoside Hydrolases
keywords: Cell wall; Co-expression network; Glycosyl hydrolase; Glycosyltransferase; Rice; Transcription factor